A simple model of co-evolutionary dynamics caused by epistatic selection

Epistasis is the dependency of the effect of a mutation on the genetic background in which it occurs. Epistasis has been widely documented and implicated in the evolution of species barriers and the evolution of genetic architecture. Here we propose a simple model to formalize the idea that epistasis can also lead to co-evolutionary patterns in molecular evolution of interacting genes. This model epistasis is represented by the influence of one gene substitution on the fitness rank of the resident allele at another locus. We assume that increasing or decreasing fitness rank occur equally likely. In simulations we show that this form of epistasis leads to co-evolution in the sense that the length of an adaptive walk between interacting loci is highly correlated. This effect is caused by episodes of elevated rate of evolution in both loci simultaneously. We find that the influence of epistasis on these measures of co-evolutionary dynamics is relatively robust to the details of the model. The main factor influencing the correlation in evolutionary rates is the probability that a substitution will have an epistatic effect, but the strength of epistasis or the asymmetry of the initial fitness ranks of the alleles have only a minor effect. We suggest that covariance in rates of evolution among loci could be used to detect epistasis among loci.     

Assessing the fitness landscape revolution

According to Pigliucci and Kaplan, there is a revolution underway in how we understand fitness landscapes. Recent models suggest that a perennial problem in these landscapes—how to get from one peak across a fitness valley to another peak—is, in fact, non-existent. In this paper I assess the structure and the extent of Pigliucci and Kaplan’s proposed revolution and argue for two points. First, I provide an alternative interpretation of what underwrites this revolution, motivated by some recent work on model-based science. Second, I show that the implications of this revolution need to carefully assessed depending on question being asked, for peak-shifting is not central to all evolutionary questions that fitness landscapes have been used to explore.

Sewall Wright’s adaptive landscapes: 1932 vs. 1988

Sewall Wright introduced the metaphor of evolution on “adaptive landscapes” in a pair of papers published in 1931 and 1932. The metaphor has been one of the most influential in modern evolutionary biology, although recent theoretical advancements show that it is deeply flawed and may have actually created research questions that are not, in fact, fecund. In this paper I examine in detail what Wright actually said in the 1932 paper, as well as what he thought of the matter at the very end of his career, in 1988. While the metaphor is flawed, some of the problems which Wright was attempting to address are still with us today, and are in the process of being reformulated as part of a forthcoming Extended Evolutionary Synthesis.

Early stages of beta2-microglobulin aggregation and the inhibiting action of alphaB-crystallin

Static and dynamic light scattering experiments on extremely clean (nanofiltered) samples of the well-known amyloidogenic protein beta2-microglobulin (R3Abeta2m and WTbeta2m) evidence the self-assembly of early aggregates showing unexpected features. Further, we find that alphaB-crystallin effectively inhibits aggregation of beta2m in a far less than stoichiometric proportion, from 1:60 alphaB-crystallin monomer to beta2m monomer ratio, down to at least a 1:2 x 10(3) alphaB-crystallin oligomerto beta2m monomer ratio. Therefore, inhibition of the early stage of beta2m aggregation by alphaB-crystallin does not necessarily require a mechanicistic chaperon-like action implying one-to-one binding. This highlights the role of the free energy landscape of the system and of related modifications of solute-solvent thermodynamics caused by co-solutes, in agreement with recent work from our and other laboratories.     

Importance of boreal grasslands in Sweden for butterfly diversity and effects of local and landscape habitat factors

A widespread decline in biodiversity in agro-ecosystems has been reported for several groups of organisms in Western Europe. The butterfly fauna was studied in 60 selected semi-natural grasslands in a coniferous-dominated boreal landscape in south-eastern Sweden. The aim was to investigate how butterfly assemblages were affected by the amount of semi-natural grasslands in the surrounding landscape. Furthermore, we wanted to determine if semi-natural grasslands in boreal landscapes harboured species otherwise declining in other parts of Europe. For each study site, the amounts of semi-natural grasslands in the landscape within radii of 500, 2,000 and 5,000 m were studied. Nine local habitat factors were also recorded. Only the amount of semi-natural grasslands within a 5,000 m radius could explain a significant part of the variation in butterfly composition, but there was no clear relationship between the amount of semi-natural grassland and butterfly diversity. Instead, this study showed that local habitat quality was very important for butterfly diversity at individual sites. Flower abundance, sward height and herb composition were the most important local factors. Patches surrounded by a small amount of semi-natural grasslands had high butterfly diversity, contrary to expectations. This may be explained by the fact that forest habitat provides a matrix with several features suitable for butterflies. The butterfly fauna was rich in species representative of low-productivity grasslands, species that are declining in other countries in Western Europe.     

The trade-off between vegetative and generative reproduction among angiosperms influences regional hydrochorous propagule pressure

Aim Local communities are subject to spatiotemporal contingencies of landscape processes; community assembly is thus often considered to be unpredictable and idiosyncratic. However, evolved trade‐offs of species’ life histories may set distinct constraints on the assembly of species communities. In plants, the recruitment and invasion success of species into communities depend primarily on the number of propagules available and on their generative or vegetative character. Life‐history trade‐offs prevent individual plants from producing large numbers of both generative and vegetative propagules, but it is not clear whether this constrains their availability at the landscape scale. We thus tested whether: (1) the observed relationship between generative and vegetative propagules deviates from the null expectation stating that species contributing the bulk of generative propagules to the propagule rain should also contribute the bulk of vegetative propagules; and (2) whether vegetative and generative propagule pressures are negatively correlated once species abundance in the regional pool is accounted for. Location A large riparian landscape in the Netherlands. Methods Analyses were based on an extensive trapping of floating propagules (214,049 propagules of 47 species), and a rough proxy of species abundance across the entire pool. We used both species and phylogenetically independent contrasts as data points, and accounted for variation in size of generative propagules. Results Both hypotheses were confirmed. Numbers of generative and vegetative propagules trapped per species were significantly negatively correlated (r = ?0.33; t₄₅ = ?2.61, P = 0.006) and thus strongly deviated from the null expectation. This was confirmed by analyses accounting for variation in species abundance across the species pool, and in the size of generative propagules. Main conclusions The results indicate that plant recruitment and community assembly across streams may be influenced by the way individual plants allocate their resources between competing life‐history functions. Life‐history evolution across angiosperms might thus have constrained the present‐day assembly of local communities.     

Biodiversity in agricultural landscapes: The effect of apple cultivar on epiphyte diversity

In natural systems, extended phenotypes of trees can be important in determining the species composition and diversity of associated communities. Orchards are productive systems where trees dominate, and can be highly biodiverse, but few studies have considered the importance of tree genetic background in promoting associated biodiversity. We tested the effect of apple cultivar (plant genetic background) on the diversity and composition of the associated epiphytic bryophyte community across a total of seven cultivars in five productive East Anglian orchards where each orchard contained two cultivars. Data were collected from 617 individual trees, over 5 years. Species richness and community composition were significantly influenced by both orchard and cultivar. Differences among orchards explained 16% of the variation in bryophyte community data, while cultivar explained 4%. For 13 of the 41 bryophyte species recorded, apple cultivar was an important factor in explaining their distribution. While the effects of cultivar were small, we were able to detect them at multiple levels of analysis. We provide evidence that extended phenotypes act in productive as well as natural systems. With issues of food security ranking high on the international agenda, it is important to understand the impact of production regimes on associated biodiversity. Our results can inform mitigation of this potential conflict.     

The genetics of adaptation to discrete heterogeneous environments: frequent mutation or large‐effect alleles can allow range expansion

Range expansions are complex evolutionary and ecological processes. From an evolutionary standpoint, a populations' adaptive capacity can determine the success or failure of expansion. Using individual‐based simulations, we model range expansion over a two‐dimensional, approximately continuous landscape. We investigate the ability of populations to adapt across patchy environmental gradients and examine how the effect sizes of mutations influence the ability to adapt to novel environments during range expansion. We find that genetic architecture and landscape patchiness both have the ability to change the outcome of adaptation and expansion over the landscape. Adaptation to new environments succeeds via many mutations of small effect or few of large effect, but not via the intermediate between these cases. Higher genetic variance contributes to increased ability to adapt, but an alternative route of successful adaptation can proceed from low genetic variance scenarios with alleles of sufficiently large effect. Steeper environmental gradients can prevent adaptation and range expansion on both linear and patchy landscapes. When the landscape is partitioned into local patches with sharp changes in phenotypic optimum, the local magnitude of change between subsequent patches in the environment determines the success of adaptation to new patches during expansion.     

Comparative landscape genetics of two frugivorous bats in a biological corridor undergoing agricultural intensification

Agricultural intensification in tropical landscapes poses a new threat to the ability of biological corridors to maintain functional connectivity for native species. We use a landscape genetics approach to evaluate impacts of expanding pineapple plantations on two widespread and abundant frugivorous bats in a biological corridor in Costa Rica. We hypothesize that the larger, more mobile Artibeus jamaicensis will be less impacted by pineapple than the smaller Carollia castanea. In 2012 and 2013, we sampled 735 bats in 26 remnant forest patches surrounded by different proportions of forest, pasture, crops and pineapple. We used 10 microsatellite loci for A. jamaicensis and 16 microsatellite loci for C. castanea to estimate genetic diversity and gene flow. Canonical correspondence analyses indicate that land cover type surrounding patches has no impact on genetic diversity of A. jamaicensis. However, for C. castanea, both percentage forest and pineapple surrounding patches explained a significant proportion of the variation in genetic diversity. Least‐cost transect analyses (LCTA) and pairwise G″st suggest that for A. jamaicensis, pineapple is more permeable to gene flow than expected, while as expected, forest is the most permeable land cover for gene flow of C. castanea. For both species, LCTA indicate that development may play a role in inhibiting gene flow. The current study answers the call for landscape genetic research focused on tropical and agricultural landscapes, highlights the value of comparative landscape genetics in biological corridor design and management and is one of the few studies of biological corridors in any ecosystem to implement a genetic approach to test corridor efficacy.     

Assessment of the resilience of socio-ecological production landscapes and seascapes: A case study from Lefke Region of North Cyprus

The purpose of this study is to assess the resilience of socio-ecological production landscapes and seascapes (SEPLS) of Lefke Region in North Cyprus in the face of disturbance factors (e.g. drought, urbanization and land abandonment) by adopting a set of indicators. The main objectives of the study include measurement of the respective resilience of the ecological, social and agricultural systems of the SEPLS by using relevant indicators. The method of the study consists of three parts: (i) conceptualization of the resilience of the SEPLS of Lefke Region to address the key systems (ecosystem, agricultural and social), their hierarchical structures, components and interrelations; (ii) development of a set of suitable resilience assessment indicators for these systems; (iii) for the development of resilience assessment indicators a participatory approach was designated to collect the relevant data. Accordingly, a multiple-choice questionnaire – consisting of 5 choices – was prepared and relevant data were collected from December 2015 to March 2016 in 12 villages through personal interviews with 106 respondents.The respondents have expressed their preferences by selecting the most suitable choice in 5 which were ordered from the lowest to the highest degree of resilience (1–5 point scale). The results of the evaluation revealed that the average values (importance) of the ecological, agricultural and social resilience are respectively 2,87 (low), 3,44 (moderate) and 2,53 (low) out of maximum 5-points. The overall resilience of the SEPLS was estimated to be low with a 2,94 magnitude. Finally, some conclusions (e.g. integrated landscape management) for strengthening the resilience of the SEPLS in Lefke Region in terms of biodiversity conservation, agricultural production and sustainable livelihood development were drawn based on the major findings of the study.It is expected that the findings and conclusions of this study can draw attention of policy makers and natural resource managers on building and strengthening the resilience of the SEPLS of Lefke Region in terms of biodiversity conservation, sustainable agricultural production and livelihood development.